scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
Hamid Beiki ◽  
Derek M Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

Abstract Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals Chromosome-level reference genome of the jellyfish Rhopilema esculentum

GigaScience ◽  
2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Yunfeng Li ◽  
Lei Gao ◽  
Yongjia Pan ◽  
Meilin Tian ◽  
Yulong Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary History ◽  
Reference Genome ◽  
Protein Coding ◽  
Fishery Resource ◽  
Rhopilema Esculentum ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
History Of ◽  
Chromosome Level

Abstract Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

2019 ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
H. Beiki ◽  
Derek M. Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

AbstractThe domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 115 ◽  
Author(s):  
Josefin Stiller ◽  
Guojie Zhang
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Genomic Data ◽  
Genome Project ◽  
Tree Of Life ◽  
Long Read ◽  
Recent Developments ◽  
Genome Assemblies ◽  
Avian Genomes ◽  
Chromosome Level

Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up.

9/11 and Armageddon: the Christian Right and George W. Bush

2003 ◽  
Vol 2 (1) ◽  
pp. 33-50
Author(s):  
Göran Gunner
Keyword(s):  
New York ◽  
Christian Right ◽  
Political Life ◽  
Religious Leader ◽  
The European Union ◽  
The World ◽  
Mega Church ◽  
The Usa ◽  
Jerry Falwell ◽  
High Degree

Authors from the Christian Right in the USA situate the September 11 attack on New York and Washington within God's intentions to bring America into the divine schedule for the end of the world. This is true of Pat Robertson and Jerry Falwell, and other leading figures in the ‘Christian Coalition’. This article analyses how Christian fundamentalists assess the roles of the USA, the State of Israel, Islam, Iraq, the European Union and Russia within what they perceive to be the divine plan for the future of the world, especially against the background of ‘9/11’. It argues that the ideas of the Christian Right and of President George W. Bush coalesce to a high degree. Whereas before 9/11 many American mega-church preachers had aspirations to direct political life, after the events of that day the President assumes some of the roles of a mega-religious leader.

Introduction

2017 ◽  
Author(s):  
Detlef Pollack ◽  
Gergely Rosta
Keyword(s):  
The Netherlands ◽  
Western Europe ◽  
West Germany ◽  
World Today ◽  
The World ◽  
Degree Of Stability ◽  
Important Exception ◽  
High Degree ◽  
Religious Landscape

In recantation of his earlier approach, Peter L. Berger now claims: ‘The world today, with some exceptions […], is as furiously religious as it ever was, and in some places more so than ever.’ The most important exception that Berger refers to is Western Europe. The introduction to Part II provides an overview of the religious landscape in Western Europe. The data show that the current religious situation in the countries of Western Europe is in fact subject to considerable variation. It would therefore be erroneous to describe Western Europe as secularized. At the same time, the data reveal that there have been clear secularization tendencies over the last few decades. To grasp the diversity of religious tendencies, Part II deals with three cases: West Germany with moderate downward tendencies, Italy with a considerably high degree of stability, and the Netherlands displaying disproportionately strong secularizing tendencies.

scholarly journals A new species of Ampulicomorpha Ashmead from Eocene French amber, with a list of fossil and extant Embolemidae (Insecta: Hymenoptera) of the world

2020 ◽  
Vol 191 ◽  
pp. 20
Author(s):  
Cédric Chény ◽  
Elvis Guillam ◽  
André Nel ◽  
Vincent Perrichot
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
Western Europe ◽  
Distribution Map ◽  
Single Female ◽  
Fossil Species ◽  
The World ◽  
Poor Group ◽  
A New Species ◽  
Eocene Amber

Embolemidae is a cosmopolitan but species-poor group of chrysidoid wasps with a scarce fossil record, despite a long evolutionary history since at least the Early Cretaceous. Here, the new species, Ampulicomorpha quesnoyensis sp. nov., is illustrated and described based on a single female found in Early Eocene amber of Oise (France). The new species is compared with the three other known fossil species of the genus, and a key to all fossil species of Ampulicomorpha is provided. This is the third European fossil species of Ampulicomorpha, which suggests that the genus was once well established in Western Europe while it is more widely distributed in the Eastern Palaearctic region today. A list of all fossil and extant Embolemidae of the world, as well as a map of their geographical distribution map, are provided.

scholarly journals The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nathalie Raharimalala ◽  
Stephane Rombauts ◽  
Andrew McCarthy ◽  
Andréa Garavito ◽  
Simon Orozco-Arias ◽  
...  
Keyword(s):  
Wild Species ◽  
Illegitimate Recombination ◽  
Recombination Mechanism ◽  
Comparative Analyses ◽  
Robusta Coffee ◽  
Caffeine Synthase ◽  
The World ◽  
Decaffeinated Coffee ◽  
Chromosome Level

AbstractCaffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

scholarly journals Ophiocordyceps salganeicola, a parasite of social cockroaches in Japan and insights into the evolution of other closely-related Blattodea-associated lineages

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
João P. M. Araújo ◽  
Mitsuru G. Moriguchi ◽  
Shigeru Uchiyama ◽  
Noriko Kinjo ◽  
Yu Matsuura
Keyword(s):  
Genetic Similarity ◽  
Evolutionary History ◽  
Fungal Species ◽  
Evolutionary Relationships ◽  
Ryukyu Archipelago ◽  
Phylogenetic Placement ◽  
The Social ◽  
Host Jump ◽  
High Degree ◽  
A New Species

AbstractThe entomopathogenic genus Ophiocordyceps includes a highly diverse group of fungal species, predominantly parasitizing insects in the orders Coleoptera, Hemiptera, Hymenoptera and Lepidoptera. However, other insect orders are also parasitized by these fungi, for example the Blattodea (termites and cockroaches). Despite their ubiquity in nearly all environments insects occur, blattodeans are rarely found infected by filamentous fungi and thus, their ecology and evolutionary history remain obscure. In this study, we propose a new species of Ophiocordyceps infecting the social cockroaches Salganea esakii and S. taiwanensis, based on 16 years of collections and field observations in Japan, especially in the Ryukyu Archipelago. We found a high degree of genetic similarity between specimens from different islands, infecting these two Salganea species and that this relationship is ancient, likely not originating from a recent host jump. Furthermore, we found that Ophiocordyceps lineages infecting cockroaches evolved around the same time, at least twice, one from beetles and the other from termites. We have also investigated the evolutionary relationships between Ophiocordyceps and termites and present the phylogenetic placement of O. cf. blattae. Our analyses also show that O. sinensis could have originated from an ancestor infecting termite, instead of beetle larvae as previously proposed.

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